Light In The Window
by immafermata
Summary: Mulder has to leave Scully and William. Scully's thoughts on everything that happens in the ninth season.


**Title: **Light In The Window

**Rating: **T

**Spoilers: **Pretty much the entire series, but especially the ninth.

**Pairing: **MSR

**Disclaimer: **I don't own them. Sad, but true.

**Summary: **Mulder has to leave Scully and William. This revolves around most of the events of the ninth season.

**A/N: **I have been out of writing fanfiction for three years. I have finally made my way back to the dark side. This is my first attempt at The X-Files. Please, let me know your thoughts. The song belongs to my uncle. I couldn't believe how perfect it fit for our dynamic duo.

_A shadow touched by the light disappears_

_Just like the love we have known_

_Our love has been washed by the rain and the tears_

_Till farther apart we have grown  
_

The steady rush of the water in the next room almost calmed me with its steady pulse. Almost. The conversation Mulder and I just had left me feeling quite empty. I knew this was something that could not be avoided, had to be done. However, that did not help my heavy heart.

I thought back to the conversation we just had about what had to be done. For the past two days we had been dancing around the subject, trying to enjoy the time that we finally had to be ourselves together. But, there was not much time to be wasted. Mulder's life was in danger. There was nothing that could be changed about that. If he did not disappear, who knows what could happen to not only him, but this family that we had now. As difficult as the decision was, we both knew that it was right. Mulder had to go into hiding. There could be no contact. My eyes welled up at the thought.

William started to cry in his crib and he brought me back to reality. I looked up toward the bathroom. Not wanting to disturb Mulder in the shower I quickly closed the door to the bathroom, giving a glance in his direction before I did so. As much as I wanted to spend every second I could with him before he left, I knew that we both needed a moment to compose ourselves before the inevitable happened.

I turned to face my son. My miracle. I picked him up and began to rub his back, whispering soothing nothings in his ear. "It's okay. You're alright. Everything is going to be okay." I almost scoffed at my words. Everything was not going to be okay.

I walked into the living room rubbing small circles on William's back. This was almost as much of a comfort to me as it was to him. His cries slowly subsided as I continued to whisper in his ear. I heard the water stop running as I looked down at the pile of black bags taking up half of the walkway.

I could not believe that this was happening. It was always MulderandScully, MrandMrsSpooky, TheDreamTeam. Never apart. How could we be separated now? After everything that we have been though together we have somehow managed to escape with our sanity. Now that everything almost seemed normal, it was being torn apart once more. It almost seemed as if nothing good with us could ever stay.

I heard Mulder step out of the shower and go into my- our bedroom to get changed. When I looked up from the ominous black bags he was standing there in jeans pulling one of his infamous gray t-shirts over his head. His hair was still wet, spiked up from attempting to dry it with the towel. God. I was going to miss the sight of him.

He attempted a smile, as did I, but they both faded before they were even visible. I was the first to speak. "I can't believe this is happening." I said softly enough that for a second I wondered if he heard me.

His beautiful lips turned down in the corners. "I know." He said striding across the small room to meet me. "It won't be forever. I am going to make sure of it." He said in a voice just as quiet. He looked me straight in the eyes. _I promise._ The look said.

I sighed and placed my hand on his arm. I looked up at him. _I know._

He engulfed William and myself into his arms and rested his head on the top of mine. "You two are my home now. I don't know how I am going to do this." He rasped against my hair.

I moved backward so I could look him in the eye. "We will get through this." I took his hand in my own, and led him into the bedroom to put William back in his crib. As soon as William was safely in the comfort of his blanket I turned around and pressed myself up against Mulder in an embrace. My arms slid around his back and I squeezed as tight as I dared. His arms came around me, in an equally strong embrace. He kissed the top of my head and I looked up at him. I gave him a look with nothing but the most pure love I could. He returned the gaze as I closed my eyes and pressed my lips against his. This couldn't be the end.

We broke apart and I put my head on his chest. He rubbed my back, almost as I had just done to our child. Everything came full circle. We stood there, not letting go of each other for I could not even guess how long. The light in the room started to become deeper, and the shadows grew longer. This can't be happening.

"As much as I don't want to say it, I think I better get going." Mulder said as his voice cracked.

Tears welled in my eyes. I looked up at him and tears started to fall freely as I saw his eyes well up. We kissed each other. Passionately. William looked up at us and started to gurgle cheerfully. Happy to see his parents enjoying a moment. Little did he know he would not be seeing his father for who knew how long.

We broke apart and Mulder looked down at William. He reached across me to pick the little peanut up. He rocked his arms back and forth as he gazed down into our miracle's eyes. "Now that I'm not going to be here, you're the man of the house. Make sure you take extra special care of your mommy. I know you will." He said kissing William as he gently rubbed his finger on his son's cheek.

With one more kiss he placed William back into the crib. He turned his gaze to me. I smiled through the tears. I couldn't wait for the moment that he would come back to raise our child. He placed his hand at the base of my neck and pulled me to him for another kiss. I reached up and placed my hand at the base of his neck as we clasped our free hand between us.

As we broke apart he gave me a sorrowful look. "I have to go." He whispered.

"I know." I whispered back.

We walked back into the living room looking at the ground. This was it. The final goodbye. He picked up the bag that he was taking with him and put it next to the door. The rest was staying here for when he returned. We could be whole once more living in a home together. He turned to face me a final time. "I love you. More than anything."

"I love you too. Always and forever." I responded to him. He pulled me in for one last earth shattering kiss. As we slowly fell apart his gaze caught mine. _I love you. _He wiped a tear away from my cheek. With one final kiss he strode to the door. His shadow long and taught across the floor. He picked up his bag and with one last "I love you," opened the door, disappeared through it, and was gone.

I sunk to the floor sobbing.

_So I'll keep a light in the window for the love that we have_

_I know that you're going away_

_Knowing is not the same as believing you'll go_

_By the light near the window I pray_

_To keep this love from burning away  
_

He was gone. Gone. Gonegonegone. As many times as I said it, I still couldn't get myself to believe it.

The first night alone was without a doubt the worst. I put William down to sleep and changed into my nightclothes from the night before. They still smelled of him. I laid down on my side of the bed and pulled the covers up to my chin. I pulled _his_ pillow to my face, holding it there, and smelled. The tears fell freely. It was so lonely in this huge bed all by myself. My hip ached to have Mulder's hand there, as he did every night. Keeping me close. Guarding me. Protecting me.

The tears turned into sobs rather quickly. I was afraid William would soon join me, but he didn't make a sound all through the night. Sleep was elusive as I lay on my side pretending I was staring into my beloved's peaceful sleeping face.

No matter how long Mulder had to be gone it didn't matter. I kept my thoughts to the moment when I could be enveloped in his arms once more. I awaited the day where I could kiss him and tell him I loved him. The moment could not come soon enough.

_Yesterdays and some days just pass through my mind_

_And they keep my head spinning round_

_You do not have to be cruel to be kind_

_Just be easy when you let me down  
_

I sat with William in my arms as I started out the window. I had taken the phone off the hook, hoping that once he fell asleep, he wouldn't be disrupted by the loud shrill cry of the phone. I rubbed his cheek and slowly rocked him back and forth willing him to sleep. It was amazing how he sleep peacefully though the night and could fall back asleep again right now. How I wished I could do the same.

I stare at the blue sky dotted with white whips and my thoughts immediately drifted to Mulder.

The day we met. The first time opened up with each other in that motel room. My father dying. His father dying. My abduction. My cancer. Undercover work. California. All I could hear were his words. "You are my one in five billion." "Even when the world was falling apart, you were my constant… my touchstone."

I then whispered "And you are mine," as a tear slid down my cheek.

A knock on the door brought me out of my reverie. There were only four people that it could be, and none of them were who I needed. My mind wandered to Skinner, Doggett, Reyes, and my mother. I sighed, wondering who it was, not in the mood to deal with any one of them right now.

I stood up and placed the sleeping William in his cradle and went to the front door, looking through the peephole. Doggett. What the hell did he want? However, once I had a look at his expression I knew something was wrong. I opened the door and immediately said "What? What's the matter?"

Doggett gave a look of confusion. "What's the matter? I've been trying to call you." He said worried.

"The phone is off the hook because of the baby." I stated plainly.

"Well I got panicked that you weren't going to be here. That you left too." Doggett said getting angry. Great. We were going to play this game.

I gave him a knowing look. "Come in." He stepped over the threshold and I closed the door turning to meet his gaze. I did not need to be having this conversation right now.

"I'm looking for Mulder." He said with no pretense. "I went to his apartment."

I nodded, already seeing where this was going. "I know."

"Where'd he go?" Doggett sighed. I looked over his shoulder, not meeting his eye, shaking my head. "Dana." He said, not wanting to wait. "Where'd he go?"

"He's gone." I breathed. That was the first time I actually said it out loud. It hurt more than I thought it possibly could. I looked up into Doggett's eyes. "He's just gone." I nodded, knowing that I could say no more.

Doggett looked away from me and sighed.

xxx

There was that knock again. Holding William in one arm I looked through the peephole. Doggett. Again. I sighed, opening the door for him, trying to prepare myself for whatever was about to happen.

"I'm really sorry, I… Dana, I need your help." He said before the door was fully open.

I knew exactly what he meant. "I don't know how to find him." I replied, the defeat clear in my voice.

I shook my head and walked away from the door, leaving it open, knowing that he would follow me inside. I strode across the room, headed to my bedroom to set William down. Doggett closed the front door.

"This doesn't make any sense, Mulder leaving you here all alone. Just walking out on you. Not telling you where or why."

Was he serious? He didn't know anything about what was going on. He barely even knew us. "It makes sense in its own way. That's all I can tell you." I replied from the bedroom.

"Then tell me why you can't trust me." Doggett said. It sounded like he was standing right outside the door. "Everything I did to protect you when you thought your baby was in danger. What changed? Why is it suddenly now I'm the enemy?" Oh, I don't know. Let's see. There are people trying to kill Mulder. The government has eyes and ears everywhere. If they knew that I trusted someone other than Mulder maybe they would get to them too. I didn't want to wish that on Doggett, Reyes, or Skinner. I tried to distance myself. If that seemed like I didn't trust them, well, all the better for them. Maybe they would back off.

I placed William down in his cradle coming out to face Doggett. "Let it go, John. Drop it. Please." I said shortly.

Walking back into the living room, he continued. "These people tried to kill me, they tried to kill A.D. Skinner, they would have killed Mulder too. They're still out there, Dana."

_He _is trying to tell _me_ that they're still out there. Like I needed another reminder. "Exactly right, and they are unstoppable, and they are inside the FBI."

"You know something you're not telling me. Mulder knows something." Of course I do. Of course Mulder does. Why else would he have to leave the only thing he has ever known of as a home? "How long can you hide from him?" He gave me a piercing stare. I had to look down. "Null Roar. This old military buddy of mine, told me your pregnancy was a result of a government cloning experiment to try to create what he called a super soldier."

How dare he. How dare he say this to me. Why could he know? This is something that Mulder and I discussed in private as a possibility. Maybe he was trying to help, but this was not the way to go about doing it. He wasn't going to get me to tell him something by being this cruel. I knew that something was different with William, but after those super soldiers didn't take him, I wanted to believe that everything was okay now. Even though I knew it wasn't. "I don't want to hear this. Look, there is nothing to any of this." I said trying to dismiss him.

"Null Roar, my buddy, was one of the men that tried to kill us in the FBI garage." He said. He was _not _trying to play the sympathy card with me.

"My baby, my son, is fine." Maybe if I said it enough, it would be true.

"I hope to God that's true. I just don't want to pretend." He said staring into my eyes. I felt as if he did so any longer he would see right through me and my façade.

"I'm going to ask you to leave." I saw the instant regret in his face. "I'm going to ask you to leave, and not come back here." He stared at me before slowly walking to the door, and leaving.

I stared at him until the door closed, and gave a harrowing sigh. Dana Scully: pushing everyone away extraordinaire.

xxx

I awoke with a start. William was crying. I rolled over to face him, and for a second I thought I was still asleep dreaming. William's wooden star mobile, hanging above him was spinning around and around by itself. I sat up in bed, not able to comprehend. I stood up and looked down into the crib. William was staring straight up, crying, looking at it. I stopped it with my hand. This was unreal. I let go, and it started to move again, as Williams cries got louder. This was not happening.

I ran to the phone and dialed the only people I knew I could trust. Monica picked up the phone. "Monica Reyes."

"Uh, yeah. It's Scully." I managed to get out. I was staring at William in his crib. The mobile had stopped moving. As did the cries.

"Dana? What's wrong are you alright?" She said worriedly through the phone.

"Is… Agent Doggett there?" I asked quickly.

"Yeah, he's right here with me." She replied.

I heard her pass the phone to him. "Dana, is something wrong?"

I looked to William. "Yeah. Yeah, some_thing._ Um, I think I might have been wrong… telling you to drop your investigation."

Understanding my implications he said "I… didn't drop it. In fact, we found something. We're not sure how it fits, but we're working on it."

"What is it?" I said shortly.

"A body." Was his response.

_So I'll keep a light in the window for the love that we have_

_I know that you're going away_

_Knowing is not the same as believing you'll go_

_By the light near the window I pray_

_To keep this love from burning away  
_

The months that followed got harder and harder. Something was definitely not normal with William. I didn't know how to explain it. All I knew is that he was going to be here. No matter what it took I, and when he got back, Mulder was going to protect him.

I decided I was going to start writing in a journal. It was going to be for William when he was old enough to understand. I wanted to make sure that when he was older he knew everything. I didn't want to miss a single detail, so I was writing it all down for him. I cracked open the new book, relishing in the sound and the feel of opening a new book.

He was asleep in the crib as I verbalized what I was slowly writing down. "One day, you'll ask me to speak of a truth - of the miracle of your birth. To explain what is unexplained. And if I falter or fail on this day, know there is an answer, my child, a sacred imperishable truth, but one you may never hope to find alone. Chance meeting your perfect other, your perfect opposite - your protector and endangeror. Chance embarking with this other on the greatest of journeys - - a search for truths fugitive and imponderable. If one day this chance may befall you, my son, do not fail or falter to seize it. The truths are out there. And if one day you should behold a miracle, as I have in you, you will learn the truth is not found in science, or on some unseen plane, but by looking into your own heart. And in that moment you will be blessed - and stricken. For the truest truths are what hold us together, or keep us painfully, desperately apart."

xxx

I entered the coffee shop that I had designated to checking my e-mail after I was done taking a walk with William. As I logged on I could not believe my eyes. Mulder. He sent me an e-mail. I clicked it, almost unable to breathe.

"Dearest Dana:

I have resisted contacting you for reasons I know you appreciate. But, to be honest, some unexpected dimensions of my new life are eating away any resolve I have left. I'm lonely, Dana, uncertain of my ability to live like this. I want to come home, to you, to William."

I looked to William, tears prickling my eyes, as I clicked the reply button.

"I am physically shaking right now, seeing your words. Wishing it were you speaking to me. I want so badly to see you too, but you are still not safe here." I clicked send, a tear rolling down my cheek.

xxx

As the events of the next few days unfolded, I kept the printed out version of Mulder's e-mail to me, looking at it when I felt particularly lonely, which happened to be quite often. After being attacked from all directions, I finally caved, having no resolve myself. I sent for Mulder. I understood the risks, and knew what could happen, but my reasons were mostly selfish. I couldn't bear to be apart from him any longer. It was physically making me ill.

I stood on the platform of the train station unable to believe it was finally here. For getting three hours of sleep last night, working all day, and it being midnight, I was more wide awake than I remember being in a long time. I couldn't believe that in just a few short moments Mulder would be in my arms. I would be able to hug and kiss him and for that moment everything in my life would be okay. There would be nothing other than us. Perhaps, he would be able to stay. Oh, how I longed to touch him.

I looked down at my watch. Almost time. Monica came from around the corner. The man's name I didn't know, and wasn't allowed to, spray painted the camera that showed the happenings on the platform. It then began to fill with people hurrying about. I couldn't believe that other people were actually living normal lives. They were on their way for a vacation, or a business trip. It was all too surreal.

The platform intercom then crackled to life. "May I have your attention please? The southbound 112 is now arriving. Southbound 112 now arriving. Please stay clear of the platform until the train comes to a full stop."

As I heard the dinging bells of the arriving train my eyes filled with tears. I couldn't believe the moment was finally here. I was finally going to see him. He would be stepping off the train any moment. Of course, then everything went to hell. When did it not?

The man helping us pulled his gun as the shadow man approached. Monica yelled "No, Scully!" Running towards me as I realized what was happening. It all seemed to be going in slow motion. People ducked down and I finally realized Monica was running to get me down as well. The shadow man pulled the trigger and hit our friend straight in the chest. We looked up at him as he approached us, gun still drawn. There were then two shots as they hit him in the leg in the chest from behind. Looking behind him, I saw that it was John.

The shadow man fell off the platform onto the tracks below us as soon as he did so the train enveloped his body. However… wait… it wasn't stopping. Everything went back into real time as I realized the train wasn't stopping. I heard someone in uniform yelling into a walkie talkie, which I assumed had a partner on the train. "Two men shot! Two men shot! Keep rolling! " I ran toward him.

"Stop the train!" I yelled.

"Keep rolling!"

"I'm a federal agent!" I tried again.

"Keep rolling!"

I stared at him unable to believe what was happening. The moment that I had been waiting for, for much too long passed in an instant. "Mulder!" I yelled, knowing that he would not be able to hear me on the passing train. "Mulder!" I watched as the last car rolled by. I wasn't going to see him. He was gone. Again. Gonegonegone.

_All of a sudden love has gone up in thin air_

_I thought you would be there_

_With a lifetime to share_

_Now I have to go it alone_

After the fiasco that was almost seeing Mulder was done with everything had no meaning again. I knew that now it would be even longer before I saw him again. There was no way he could come home before this was all done with. Which, would probably never end. It was becoming harder and harder to keep William safe. I knew that if that could happen with trying to get Mulder here, it was only a matter of time before something equally as horrible would happen to my son.

It didn't help that he had exhibited some… strange, to say the least, powers. After the fiasco with Jeffrey Spender I wished and hoped that he was a normal child. However, I was not able to trust it. Who knew if it actually worked? And even if it did, would it still keep the horrible people away from him?

I had no other option. There was no way that William could be safe when he was with me. As much as I longed to talk it over with Mulder, there was no way to contact him. I wanted him to hold me and tell me everything was going to be alright, no matter what happened. I wanted to let him know that this was the hardest decision that I have ever had to make. It wasn't because I didn't love William. It was because I loved him too much. I wanted to tell Mulder what I was doing to my baby. Our baby. He deserved some say in what happened to his child. Didn't he? But it was months since I have had any contact with him.

Years ago I had always thought that Fox Mulder was going to be a constant in my life. Even before we were romantically involved I couldn't see myself with anyone else as a partner. We just clicked. Years later he had to leave and that constant was no longer there. However, I still had a part of him. I had a part of him in my son, whom I thought would always be there. Even after I was long gone, he would still be here. I wanted to see him grow old. Meet the love of his life. Have children. Have grandchildren. But I guess that wasn't in the cards for me.

I couldn't remember much about giving William up for adoption. All I know is that I showered him with kisses and hugs and murmurs of love, affection, and apology.

_Keep a light in the window for the love that we have_

_I know that you're going away_

_Knowing is not the same as believing you'll go_

_By the light near the window I pray  
_

Everything after that was a blur. I don't remember much of anything. I know that I stayed in my house for who knows how many days just crying. I would go into the empty room that once was a nursery thinking of what could have and should have been. I hid the journal that I had been writing in for him in my bookshelf behind _Moby Dick_. I couldn't bear to look at it.

After Mulder left I had stopped attending church, and praying. I felt as if this was some kind of punishment, that I had done something wrong and that the only happiness I had left was in my son. When William was gone I had no one else to turn to. My love for him would never fade. I'm sure that it will haunt me for the rest of my days.

I began to pray when I couldn't cry anymore. I prayed that William had a safe and long life. I prayed that somehow Mulder was okay. I prayed that somehow, someway we would end up in each other's arms once again.

_Keep a light in the window for the love that we have_

_I know that you're going away_

_Knowing is not the same as believing you'll go_

_By the light near the window I pray_

_To keep this love from burning away  
_

A buzzer rang. I knew it was because we were coming in through the open door, but I longed to it to be a buzzer at a basketball game that I was watching with Mulder. Soon enough, I told myself. "How long has he been here?" I said showing my ID as Skinner did the same behind me. The guard opened the first of the locked gates.

"I'm trying to get someone to say." Skinner replied.

"Who called you?" I asked wanting to know every detail.

"Kersh's office." Skinner said coldly.

"Who called them?" I inquired more.

"I don't know. I just know that Mulder is being held here indefinitely." Skinner replied meeting my fast strides as the gate clanked shut behind us.

"What for?" I asked turning to face him. We were in a military prison. _What _could he have done?

"The murder of a military man." Skinner said looking down at me. I gazed back up at him in disbelief.

Skinner then fell silent. After all this time, I couldn't believe this was actually happening. I silently thanked God for this moment, even if it was not a pretty one. We were finally back together. In just one moment I would have him in my arms. I don't care what the military said he did or didn't do. I know in my heart that whatever they have him in here for is just part of their witch hunt.

Another door opened before me and I couldn't believe my eyes. The man in the orange jumpsuit looked as if he were having a conversation with somebody, but there was no one there. "Mulder." I said, letting the words fall from my lips unable to comprehend he was standing right before me. He turned around.

"Dana."

**Fin.**


End file.
